mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
21 lines
786 B
Text
21 lines
786 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
|
include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
|
|
include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
|
|
|
|
workflow test_kaiju_kaiju_single_end {
|
|
|
|
input = [
|
|
[ id:'test', single_end:true ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
|
]
|
|
db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
|
|
taxon_rank = "species"
|
|
|
|
ch_db = UNTAR ( db )
|
|
KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
|
|
KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
|
|
}
|